About MAKER

MAKER is an easy-to-configure, portable genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and prokaryotic genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations with evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. Its outputs are in GFF3 or FASTA format, and can be directly loaded into Chado, GBrowse, JBrowse, WebApollo or Apollo.

For those annotating novel plant genomes, the MAKER-P pipeline is designed to make the annotation tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes. The MAKER-P website has more information on the additional protocols for plant genome annotation.

Additional MAKER options and capabilities include:

Map old annotation sets on to new assemblies.

Merge multiple legacy annotation sets into a consensus set of annotations.

Use GFF3 pass-through to include both evidence alignments and predicted gene models from algorithms not natively supported by MAKER.

MAKER is MPI-capable for rapid parallelization across computer clusters.

You can also easily integrate raw InterProScan results into MAKER, which will identify protein domains; add GO functional categories; and help assign putative gene functions to genome annotations. This data then becomes accessible as part of the GFF3 output and can be loaded into a Chado database, JBrowse, GBrowse, WebApollo or Apollo.

MAKER comes with sample data for testing purposes. See the /data directory in the download.

Installation

Documentation

By default, MAKER runs on a single computer. A parallel version, mpi_maker, is also available. To run mpi_maker you will need a message passing interface (MPI) package installed on all participating computers; try MPICH2. Remember to install MPICH2 with the --enable-sharedlibs flag set to the appropriate value .See the MPICH2 Installer's Guide for more information.

See also the MAKER-P website for documentation on the additional pipeline steps for annotating plant genomes.

Annotations

The MAKER genome annotation pipeline generates several different types of annotations, including

Ab initio gene predictions from SNAP, Augustus, FGENESH, and GeneMark

Final gene models from MAKER

EST alignments from both EXONERATE and BLASTN

Protein alignments from EXONERATE and BLASTX

Repeats from RepeatMasker and the MAKER internal RepeatRunner

Publications, Tutorials, and Presentations

Publications on or mentioning MAKER

MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. [1]

MAKER is an easy-to-configure, portable ge … MAKER is an easy-to-configure, portable genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and prokaryotic genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations with evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. Its outputs are in GFF3 or FASTA format, and can be directly loaded into Chado, GBrowse, JBrowse, WebApollo or Apollo.

For those annotating novel plant genomes, the MAKER-P pipeline is designed to make the annotation tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes. The MAKER-P website has more information on the additional protocols for plant genome annotation.

Additional MAKER options and capabilities include:

Map old annotation sets on to new assemblies.

Merge multiple legacy annotation sets into a consensus set of annotations.

Use GFF3 pass-through to include both evidence alignments and predicted gene models from algorithms not natively supported by MAKER.

MAKER is MPI-capable for rapid parallelization across computer clusters.

You can also easily integrate raw InterProScan results into MAKER, which will identify protein domains; add GO functional categories; and help assign putative gene functions to genome annotations. This data then becomes accessible as part of the GFF3 output and can be loaded into a Chado database, JBrowse, GBrowse, WebApollo or Apollo.

MAKER comes with sample data for testing purposes. See the /data directory in the download./data directory in the download. +, Review article on eukaryotic genome annotation from the MAKER team. +, MAKER with additional software for plant genome annotation +, online version of the MAKER tool + and The ant genomes were annotated using MAKER. +